Here is an idea for that.
Instead of having a flagship as being ship construction 12 and only available late in the game (since historically there have been flagships in all times) have a checkbox that can be checked in ship design [ ] IS Flagship
this would add say 20% or so extra space to the selected hulltype at extra cost and would only be available to be checked at certain conditions IE 20B pop or whatnot.
Additionally I would rather see it being based on the number of ships you have rather than the number of pop. Every 100 or 50 ships etc.
With this as the setup you can limit peaceful empires with lots of pop but few ships having almost nothing but flagships.
It would also allow for flagships at a much earlier point in the game with cruiser sizes etc and allows for more varied flagships later in the game as races that prefer smaller more manueverable ships might prefer to have a BC flagship since all their ships are BC rather than some slow clunky massive thing like their neighbors do.
[This message has been edited by Cyrien (edited 21 October 2001).]